Publications >> 1986-1994 1995-1999 2000-2004 2005-present

1. "Sink Flows of Viscoelastic Fluids", with A.B. Metzner, J. Rheo1., 30, 29 (1986).

2. "C02 Absorption in Aqueous Solutions of Sterically Hindered Amines ", with G. Astarita and K.B. Bischoff, Chem. Eng Sci., 41, 997 (1986).

3. "Boundary Layer Analysis for the Modeling of Non-Catalytic Gas-Solid Reactions", with G. Astarita, I.E.C. Research, 26, 972 (1987).

4. "A Molecular Orbital Approach to Substituent Effects in Amine - CO2 Interactions", with G. Astarita et al., J. Am. Chem. Soc., 110, 6947 (1988).

5. "A Molecular Orbital Study of the Interactions of Acrylic Polymers with Aluminum: Implications for Adhesion", with H.T. Davis, M. Tirrell, J. Polym. Sci.: Polym. Chem. Ed, 28, 3185 (1990).

6. "Energetics and Near - Surface Structure at Polymer - Metal Interfaces", with J.S. Shaffer, Polymer Preprints, 31, 546 (1990).

7. "Effect of Silicate Ratio on the Distribution of Silicate and Aluminosilicate Anions in TPA Aluminosilicate Solutions", with R.F. Mortlock et al., J. Phys. Chem., 95, 4501 (1991).

8. "The Nature of the Interactions of poly (methyl methacrylate) Oligomers with an Aluminum Surface", with J. S. Shaffer et al., J. Chem. Phys. 95, 8616 (1991).

9. "On the Existence of Non-Equilibrium, Glass-Like Structures at Strongly Interacting Polymer Solid Interfaces", with J.S. Shaffer, P.M. Adriani, Macromolecules, 24, 5226 (1991).

10. "Effects of Solvent Polarity and Temperature on the Conformational Statistics of a Simple Macrocyclic Polyether", with Y.L. Ha, J. Phys. Chem., 95, 10781 (1991).

11. "The Effects of Local Structural Relaxation on Aluminum Siting in H ZSM 5", with S.R. Lonsinger et al., Catalysis Letters, 11, 209 (1991).

12. "Progress and Future Directions in the Theory of Strongly Interacting Polymer/Solid Interfaces", Proceedings of the First International Conference on Polymer/Solid Interfaces, page 3, I.O.P. Publishing Ltd., Bristol, U.K. (1992).

13. "Segment Level Chemistry and Chain Conformation in the Reactive Adsorption of PMMA on Aluminum Oxide Surfaces", with K. Konstandinidis et al., Langmuir, 8, 1307 (1992).

14. "Structure and Dynamics at Polymer/Metal Interfaces", with P.M. Adriani, J.S. Shaffer, Polymer Preprints, 33, 613 (1992).

15. "Glassy Relaxation at Polymer Solid Interfaces", with P.M. Adriani, Macromolecules, 25, 2470 (1992).

16. "The Nature of the Interactions of Ammonium Cations with 18 Crown 6", with Y.L. Ha, J. Phys. Chem., 96, 6410 (1992).

17. "Dynamics of Relaxation at Strongly Interacting Polymer Solid Interfaces: Effects of Chain Architecture", with P.M. Adriani, J. Chem. Phys., 98, 4263 (1993).

18. "Dynamics of PMMA Chains Adsorbed on Aluminum Surfaces" with J.S. Shaffer, Macromolecules, 26, 1120 (1993).

19. "Electronic and Structural Features of the Acid Site in H ZSM 5", with S.J. Cook et al., J. Phys. Chem., 97, 6679 (1993).

20. "Complexation of Ammonium Cations with 18 Crown 6: Simulations Using Proper Potentials", with Y.L. Ha, J. Phys. Chem., 97, 11291 (1993).

21. "Diffusion of Ionic Penetrants In Charged Disordered Media", with D. Bratko, David Chandler, J. Chem. Phys., 100, 1528 (1994).

22. "Characterization of Crown Ethers as Macrocyclic Elements for Rotaxane Preparation: A Monte - Carlo Simulation", with Y.L. Ha, Chem. Eng Sci., 49, 2859 (1994).

23. "Solvation of Simple Crown Ethers using the XRISM method", with Y.L. Ha, J. Phys. Chem., 98, 11193 (1994).

24. "Surface-Induced Ordering for Adsorbed Random Block Copolymers", with L. Gutman, J. Chem. Phys., 101, 10074 (1994).

25. "Elastic Constants for Random Block Copolymers in the Strong Segregation Limit: Effects of Sequence Distribution", with G.H. Fredrickson, Macromolecules, 27, 7079 (1994).

26. "Electronic Structure Calculations for Ammonia Adsorption in H-ZSM-5", with A. Kyrlidis, A.T. Bell, S.J. Cook, J. Phys. Chem., 99, 1505 (1995).

27. "Polyelectrolyte Configuration in Disordered Media", with D. Bratko, Phys. Rev. E., 51, 5805 (1995).

28. "Phase Behavior of Random Copolymers in Quenched Random Media", with E.I. Shakhnovich, J. Chem. Phys., 103, 10751 (1995).

29. "A Field Theory for Random Copolymers Near Solid Surfaces: Analysis of Interfacial Chain Organization and Adsorption-Desorption Phase Diagram", with L. Gutman, J. Chem. Phys., 103, 10733 (1995).

30. "Schrodinger Equations and Diffusion Theory by M. Nagasawa", AIChE Journal, 41, 2665 (1995).

31. "Polymer Adsorption", with M. Tirrell, feature article in Special issue of the MRS Bulletin on Polymer Surfaces and Interfaces, 21, 28 (1996).

32. "Frozen Phases of Random Heteropolymers in Disordered Media", with D. Bratko, E.I. Shakhnovich, Phys. Rev. Letts., 76, 1844 (1996).

33. "A Numerical Study of Polyampholyte Configuration", with D. Bratko, J. Phys. Chem., 100, 1164 (1996).

34. "Local Spin-Density Functional Theory Study of Copper Ion-Exchanged ZSM-5", with B.L. Trout, A.T. Bell, J. Phys. Chem., 100, 4173 (1996).

35. "Sequence Fluctuation Dependent Adsorption-Depletion Transition for Random Heteropolymers", with L. Gutman, J. Chem. Phys., 104, 7306 (1996).

36. "Morton M. Denn - Teacher and Scholar", with A.B. Metzner, T.W.F. Russell, Chem. Eng. Educ., 30, 88 (1996).

37. "Ion-Ion Correlations in Quenched Disordered Media", with D. Bratko, J. Chem. Phys., 104, 7700 (1996).

38. “Adsorption / Freezing Transition for Random Heteropolymers Near Disordered 2-D Manifolds Due to Pattern Matching", with S. Srebnik, E.I. Shakhnovich, Phys. Rev. Letts, 77, 3157 (1996).

39. “Exotic Surface Transitions of Random Heteropolymers Near Smooth Surfaces”, with L. Gutman, J. Chem. Phys., 105, 7842 (1996).

40. “Analysis of the Thermochemistry of NOx Decomposition Over Cu-ZSM-5 Based on Quantum Chemical and Statistical Mechanical Calculations”, with B.L. Trout, A.T. Bell, J. Phys. Chem., 100, 17582 (1996).

41. “The Structure of a Random Heteropolymer in a Disordered Medium: Ensemble Growth Simulation”, with D. Bratko, E.I. Shakhnovich, J. Chem. Phys., 106, 1264 (1997).

42. “Diffusion and Reaction in ZSM-5 Studied by Dynamic Monte Carlo", with B.L. Trout, A.T. Bell, Chem. Eng. Sci., 52 , 2265 (1997).

43. “Recognition Between Random Heteropolymers and Multifunctional Disordered Surfaces", with E.I. Shakhnovich and D. Bratko, Chem. Phys. Lett., 280, 46 (1997).

44. “Density Functional Theory Calculations of the Effects of Local Composition and Defect Structure on the Proton Affinity of H-ZSM-5”, with N. Gonzales, A.T. Bell, J. Phys. Chem. B., 101, 10058 (1997).

45. “Giovanni Astarita”, with T.W.F. Russell, A. B. Metzner, Physics Today 50, 84 (1997).

46. “Polymer Adsorption on Disordered Substrates”, with E.I. Shakhnovich, Phys. Rev. Lett. 79, 4931(1997).

47. “A Simple Theory and Monte-Carlo Simulations for Recognition Between Random Heteropolymers and Disordered Surfaces”, with D. Bratko, J. Chem. Phys., 108, 1676 (1998).

48. “Freezing of Compact Random Heteropolymers with Correlated Sequence Fluctuations”, with E. I. Shakhnovich, V. S. Pande, J. Chem. Phys., 108, 1683 (1998).

49. “A Density Functional Theory Study of the Effects of Metal Cations on the Bronsted Acidity of H-ZSM-5”, with N. O. Gonzales, A. T. Bell, Catalysis Letters, 50, 135 (1998).

50. “Adsorption of Random Heteropolymers on Disordered Surfaces”, with D. Bratko, E. I. Shakhnovich, Theor. and Comp. Polym. Sci., 8, 113 (1998).

51. “Effect of Topology and Molecular Occupancy on Self-Diffusion in Lattice Models of Zeolites”, with M.O. Coppens, A.T. Bell, Chem. Eng. Sci., 53, 2053 (1998).

52. “A Density Functional Theory Study of the Interactions of H2O with H-ZSM-5, Cu-ZSM-5, and Co-ZSM-5”, with M.J. Rice, A.T. Bell, J. Phys. Chem., 102, 7498 (1998).

53. “Random Heteropolymer Adsorption on Disordered Multifunctional Surfaces: Effect of Specific Intersegment Interactions”, with S. Srebnik, D. Bratko, J. Chem. Phys., 109, 6415 (1998).

54. “Adhesion Promotion at a Homopolymer-Solid Interface Using Random Heteropolymers”, with R.E. Simmons, J. Chem. Phys., 109, 8667 (1998).

55. “Applications of Density Functional Theory to Study the Physical and Chemical Properties of Transition Metal Cation-Exchanged Zeolites”, with M.J. Rice, N.O. Gonzales, A.T. Bell, Proc. of 12th International Zeolite Conference, 1, 393-400 (1999).

56. “Microphase Ordering in Melts of Randomly Grafted Copolymers”, with S. Qi, et al., Phys. Rev. Lett., 82, 2896 (1999).

57. “Dynamic Monte-Carlo and Mean-field Study of the Effect of Strong Adsorption Sites on Self-Diffusion in Zeolites”, with M.-O. Coppens, A.T. Bell, Chem. Eng. Sci., 54, 3455 (1999).

58. “Behavior of a Random Heteropolymer in Mixed Solvents”, J. Chem. Phys. 111, 5232 (1999).

59. “Al Next Nearest Neighbor, Ring Occupation, and Proximity Statistics in ZSM-5”, with M. J. Rice, A. T. Bell, J.Catal., 186, 222 (1999).

60. “A Density Functional Theory Study of Hydrogen Recombination and Hydrogen-Deuterium Exchange on Ga/H-ZSM-5”, with N. O. Gonzales, A. T. Bell, Topics in Catalysis, 9, 207 (1999).

61. “Simulation of Biomimetic Recognition Between Polymers and Surfaces”, with A. Golumbfskie and V. Pande, Featured Article, Proc. Natl. Acad. Sci., 96, 11707 (1999).

62. “Design and Synthesis of Materials with Precise Macroscopic Properties - Theoretical and Computational Approaches to Assist Rational Design: Biomimetic Recognition and Controlling Self-Assembly Processes by Tuning Polymer Architecture”, Frontiers of Engineering, (1999).

63. “Density Functional Theory Calculations of the Oxidative Dehydrogenation of Propane on the (010) Surface of V2O5”, with F. Gilardoni, A.T. Bell, and P. Boulet, J. Phys. Chem. B., 104, 12250 (2000).

64. “Theoretical Studies of the Coordination and Stability of Divalent Cations in ZSM-5”, with M.J. Rice and A.T. Bell, J. Phys. Chem B, 104, 9987 (2000).

65. “Site Availability and Competitive Siting of Divalent Metal Cations in ZSM-5”, with M.J. Rice and A.T. Bell, J. Catal , 194, 278 (2000).

66. “Applications of Density Functional Theory to Identify Reaction Pathways for Processes Occurring in Zeolites and on Dispersed Metal Oxides”, with Jason A. Ryder et al., Stud. Surf. Sci. Catal. 130, 407-412 (2000).

67. “Density Functional Theory Study of Proton Mobility in Zeolites: Proton Migration and Hydrogen Exchange in ZSM-5”, with J.A. Ryder and A.T. Bell, J. Phys. Chem. B., 104, 6998 (2000).

68. “Theoretical Study of Polymeric Mixtures with Different Sequence Statistics: I. Ising class, Linear Random Copolymers with Different Statistical Sequences and Ternary Blends of Linear Random Copolymers with Homopolymers”, with S.Y. Qi, J. Chem. Phys., 112, 1598 (2000).

69. “Theoretical Study of Polymeric Mixtures with Different Sequence Statistics: II. Brazovskii Class, Linear Random Copolymers with Diblock Copolymers”, with S.Y. Qi, J. Chem. Phys., 112, 1598 (2000).

70. “Disordered Heteropolymers: Models for Biomimetic Polymers and Polymers with Frustrating Quenched Disorder”, Physics Reports, 342, 1 (2000).

71. "Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions", G. Wu, et al., Proc. Natl. Acad. Sci., 98, 1560 (2001).

72. "Polymer Adsorption Driven Self-Assembly of Nanostructures", with A.J. Golumbfskie, Ann. Rev. Phys. Chem., 52, 537-573 (2001).

73. "Synaptic Pattern Formation During Cellular Recognition", with S.Y. Qi et al., Proc. Natl. Acad. Sci., 98, 6548 (2001).

74. "Microphase segregation in Molten Randomly Grafted Copolymers", S.Y. Qi and N. Balsara, J. Chem. Phys., 115, 3387 (2001).

75. "The Phase Diagram of Molten Randomly Grafted Copolymers", with S.Y. Qi, J. Chem. Phys., 115, 3401 (2001).

76. "Molecular Architecture can Control Surfactant Properties of Macromolecules", with A. Kreig, et al., J. Chem. Phys., 115, 6243 (2001).

77. “Immunological Synapse Formation: Physical Chemistry Meets Cell Biology”, Science STKE PE10 (2002).

78. “Lighting up TCR Takes Advantage of Serial Triggering”, Nature Immunology, 3, 895 (2002).

79. “Correlation of a Dynamic Model for Synapse Formation with Effector Functions: Two Roads to Synapse Formation”, with S.J. Lee et al., Trends in Immunology, 23 , 492 (2002).

80. “The Synapse Assembly Model”, with S.J. Lee et al., Trends in Immunology, 23 , 500 (2002).

81. “Density Functional Study of Nitrous Oxide Decomposition over Fe and Co-ZSM-5”, with J. Ryder and A.T. Bell, J. Phys. Chem., 100, 4173 (2002).

82. “Nanomechanical Forces Generated by Surface Grafted DNA”, with M.F. Hagan and A. Majumdar, J. Phys. Chem. B, 106, 10163 (2002).

83. “Thermodynamics and Phase Behavior of Block Copolymer/Homopolymer Blends”,with Attractive and Repulsive Interactions”, with J.H. Lee et al., Macromolecules, 35, 7748 (2002).

84. “Analysis of Pattern Formation and Phase Separation in the Immunological Synapse”, with Y. Hori and S. Raychaudhuri, J. Chem. Phys., 117, 9491 (2002).

85. “Sequence Dependence of Polymer Dynamics in Disordered Media”, with S.J. Lee, J. Chem. Phys., 117, 10869 (2002).

86. “Low TCR Expression Contributes to Dynamic Multifocal Synapses in Thymocytes”, with S.J. Lee, Yuko Hori, Proc. Natl. Acad. Sci., 100, 4383 (2003).

87. “Biasing a Transition State Search for Complex Reactions”, with B. Peters et al., J. Chem. Phys., 118, 9533 (2003).

88. “Decoding Communications Between Cells in the Immune System Using Principles of Chemical Engineering”, AIChE J. , 49, 1614 (2003).

89. “In Silico Models in Molecular and Cellular Immunology: Successes, Promises, and Challenges”, with A.S. Shaw and M.L. Dustin, Nature Immunology, 4, 933 (2003).

90. “Macromolecules at Surfaces: Research Challenges and Opportunities from Tribology to Biology”, with S. Granick et al., J. Polym. Sci. Part B: Polym. Phys., 41, 2755 (2003).

91. “The Immunological Synapse Balances T Cell Receptor Signaling and Degradation”, with K.H. Lee, et al., Science, 302, 1218 (2003).

92. “An Effective Membrane Model for the Immunological Synapse”, with S. Raychaudhuri, M. Kardar, Phys. Rev. Lett., 92, 208101 (2003).

93. “Density Functional Theory Study of Benzene Oxidation over Fe-ZSM-5”, with J. Ryder et al., J. Catalysis, 220, 84 (2003).

94. “Atomistic Simulation of Kinetic Pathways for DNA Unbinding and Hybridization”, with M. Hagan et al., Proc. Natl. Acad. Sci., 100, 13922 (2003).

95. “Hybridization Dynamics of Surface Immobilized DNA”, with M. Hagan, J. Chem. Phys., 120, 4958 (2004).

96. “A Growing String Method for Determining Transition States: Comparison to the Nudged Elastic Band and String Methods”, with B. Peters et al., J. Chem. Phys., 120, 7877 (2004).

97. “CD4 Coordinates Lck Accumulation in the Immunological Synapse: Implications for the Sensitivity of T Cells to Antigen”, with Q. Li et al., Nature Immunol., 5, 791 (2004).

98. “Rate Constants from the Reaction Path Hamiltonian I: Reactive Flux Simulations for Dynamically Corrected Rates”, with B. Peters and A.T. Bell, J. Chem. Phys., 121, 4453 (2004).

99. “Rate Constants from the Reaction Path Hamiltonian II: Nonseparable Semi-classical Transition State Theory”, with B. Peters and A.T. Bell, J. Chem. Phys., 121, 4461 (2004).

100. “Signatures of the Order-Disorder Transition in Copolymers with Quenched Sequence Disorder”, with H.B. Eitouni et al., Macromolecules., 37, 8487 (2004).

101. “Order-Disorder Transitions in Crosslinked Block Copolymer Solids”, with H.Han et al., Macromolecules, 38, 1277 (2005).

102. “Movies, Measurements, and Modeling – the 3M’s of Mechanistic Immunology”, with C. Witt, S. Raychaudhuri, J. Exp. Med., 201, 501 (2005).

103. “A Dendronized Polymer is a Single Molecule Glass”, with J. Das et al., J. Phys. Chem. 109, 6535 (2005).

104. “Directed Migration of Positively Selected Thymocytes Visualized in Real Time”, with C. Witt et al., PLOS Biology, 3 (6), June (2005).

105. “Phase Segregation on Different Length Scales in a Model Cell Membrane System”, with J. Liu, S.Y. Qi, J. Phys. Chem. B, 109, 19960 (2005).

106. “Chemomechanics of Surface Stresses Induced by DNA Hybridization”, with J. Stachowiak et al., Langmuir, 22, 263 (2006).

107. “Effects of Quenched and Annealed Macromolecular Crowding on Signal Transduction in T Lymphocytes”, with J. Eide, J. Phys. Chem. B, 110, 2318 (2006).

108. “Molecular Flexibility Influences the Stimulatory Ability of Receptor-Ligand Interactions at Cell-Cell Junctions”, with Mark M. Davis et al., Proc. Natl. Acad. Sci., 103, 4416 (2006). COVER

109. “Simple Models for How Proteins Convert Chemical Energy to Mechanical Work”, with J. Eide, G.F. Oster, BioPhys. J., 90, 4281 (2006).

110. “Kinetic Pathways of Phase Transitions in Model Lipid Rafts”, with J. Liu, J.T. Groves, J. Phys. Chem. B, 110, 8416 (2006).

111. “Advances in Methods and Algorithms for a Modern Quantum Chemistry Program Package”, with Y. Shao et al., Phys. Chem. Chem. Phys., 8, 3172 (2006).

112. “Effect of Cross-linking on the Structure and Thermodynamics of Lamellar Block Copolymers”, with J. Das et al., Macromolecules, 39, 4848 (2006).

113. “A Hybrid Deterministic-Stochastic Algorithm for Modeling Cell Signaling Dynamics in Spatially Inhomogenous Environments and Under the Influence of External Fields” with D. Wylie et al., J. Phys. Chem. B, 110, 12749 (2006).

114. Sensitivity of T cells to Antigen and Antagonism Emerges from Differential Regulation of the same Molecular Signaling Module”, with D. Wylie et al., Proc. Natl. Acad. Sci., 104, 5533-5538 (2007).

115. “The Stimulatory Potency of T Cell Antigens is influenced by the Immunological Synapse”, with S. Cemarski et al., Immunity, 26, 345-355 (2007).

116. “Scaffold Proteins Confer Diverse Regulatory Properties to Protein Kinase Cascades”, with J. Locasale et al., Proc. Natl. Acad. Sci., 104, 13307-13312 (2007).

117. “Temperature dependent shape transformation of Ge nanostructures by the vapor-liquid-solid method”, with J. Das et al., J Applied Phys, 101 (2007).

118. “Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities”, with M.N. Artyomov et al., Proc. Natl. Acad. Sci., 104, 18958-18963 (2007).

119. “Tug of war at the exit door”, with M.L. Dustin, Immunity, 28, 15-17 (2008).

120. “T cell sensing of antigen dose governs interactive behavior with dendritic cells and sets a threshold for T cell activation", with S.E. Henrickson et al., Nature Immunology, 9, 282-291 (2008).

121. “Molecular Models for Amplification of T cell Signaling by Endogenous Ligands”, with S.Y. Qi et al., J. Immunol., submitted.

122. “Peptide Photolysis Yields Empty Class II MHC Products that Reveal a Role for DM in Peptide Association”, Immunity, submitted.


BOOKS:
Edited Book: “Molecular Modeling and Theory in Chemical Engineering”, Academic Press, San Diego (2001).